pipeline-manual.txt

#go in the output folder, it must exists. The image folder as well has to exists.

screen

export OMP_NUM_THREAD=20

#lunch rename script, input files have to have a specific name convention
python /home/shared_brain/BrainCode/helpers/renameFilesByNumber.py /home/shared_brain/Data/RS_PCB_Oil/PCB_78_RS/Oil124RS_Activation1

#lunch corr script
/home/shared_brain/BrainCode/cor_img 50 1 0 0.7 0 n /home/shared_brain/Data/RS_PCB_Oil/PCB60RS/Oil\ 184\ RS\ Activation\ 1 /home/shared_brain/Output/Images/RS_PCB_Oil/Oil184RS/Activation1/w50_cor.70

#split the pair file
/home/shared_brain/BrainCode/Louvain/split_files.py cor_weights_cor70.pair

#copy the make file
cp /home/shared_brain/BrainCode/Louvain/Makefile .

#remove small files!

#louvain
make

#commdy1
/home/shared_brain/BrainCode/commdy/script/ipc-gams.py louvain.gtm

#commdy2
/home/shared_brain/BrainCode/commdy/script/gamsout2color.py louvain.gtm louvain_ipc.out > louvain_ipc.gcolor

#commdy3
/home/shared_brain/BrainCode/commdy/src/color_ind2 -cost 111 louvain.gtm <louvain_ipc.gcolor >louvain_ipc-c111.color2

#Rscript
Rscript /home/shared_brain/BrainCode/Rstatistics/brainStats.R